The present invention relates generally to the detection, treatment and prevention of infectious diseases. In particular, the invention is related to compounds comprising immunogenic epitopes isolated from Mycobacterium vaccae, and the use of such compounds in vaccination or immunotherapy against infectious disease, including mycobacterial infections such as infection with Mycobacterium tuberculosis or Mycobacterium avium, and in certain treatments for immune disorders and cancer.
The present invention relates generally to the treatment and prevention of infectious diseases, and to the treatment of certain immune disorders and cancers. In particular, the invention is related to compounds and methods for the treatment and prevention of mycobacterial infections including infection with Mycobacterium tuberculosis or Mycobacterium avium. 
Tuberculosis is a chronic, infectious disease that is caused by infection with Mycobacterium tuberculosis (M. tuberculosis). It is a major disease in developing countries, as well as an increasing problem in developed areas of the world, with about 8 million new cases and 3 million deaths each year. Although the infection may be asymptomatic for a considerable period of time, the disease is most commonly manifested as a chronic inflammation of the lungs, resulting in fever and respiratory symptoms. If left untreated, significant morbidity and death may result.
Although tuberculosis can generally be controlled using extended antibiotic therapy, such treatment is not sufficient to prevent the spread of the disease. Infected individuals may be asymptomatic, but contagious, for some time. In addition, although compliance with the treatment regimen is critical, patient behaviour is difficult to monitor. Some patients do not complete the course of treatment, which can lead to ineffective treatment and the development of drug resistant mycobacteria.
Inhibiting the spread of tuberculosis requires effective vaccination and accurate, early diagnosis of the disease. Currently, vaccination with live bacteria is the most efficient method for inducing protective immunity. The most common mycobacterium employed for this purpose is Bacillus Calmette-Guerin (BCG), an a virulent strain of Mycobacterium bovis. However, the safety and efficacy of BCG is a source of controversy and some countries, such as the United States of America, do not vaccinate the general public. Diagnosis of M. tuberculosis infection is commonly achieved using a skin test, which involves intradermal exposure to tuberculin PPD (protein-purified derivative). Antigen-specific T cell responses result in measurable induration at the injection site by 48-72 hours after injection, thereby indicating exposure to mycobacterial antigens. Sensitivity and specificity have, however, been a problem with this test, and individuals vaccinated with BCG cannot be distinguished from infected individuals.
A less well-known mycobacterium that has been used for immunotherapy for tuberculosis, and also leprosy, is Mycobacterium vaccae, which is non-pathogenic in humans. However, there is less information on the efficacy of M. vaccae compared with BCG, and it has not been used widely to vaccinate the general public. M. bovis BCG and M. vaccae are believed to contain antigenic compounds that are recognised by the immune system of individuals exposed to infection with M. tuberculosis. 
Several patents and other publications disclose treatment of various conditions by administering mycobacteria, including M. vaccae, or certain mycobacterial fractions. International Patent Publication WO 91/02542 discloses treatment of chronic inflammatory disorders in which a patient demonstrates an abnormally high release of IL-6 and/or TNF or in which the patient""s IgG shows an abnormally high proportion of agalactosyl IgG. Among the disorders mentioned in this publication are psoriasis, rheumatoid arthritis, mycobacterial disease, Crohn""s disease, primary biliary cirrhosis, sarcoidosis, ulcerative colitis, systemic lupus erythematosus, multiple sclerosis, Guillain-Barre syndrome, primary diabetes mellitus, and some aspects of graft rejection. The therapeutic agent preferably comprises autoclaved M. vaccae administered by injection in a single dose.
U.S. Pat. No. 4,716,038 discloses diagnosis of, vaccination against and treatment of autoimmune diseases of various types, including arthritic diseases, by administering mycobacteria, including M. vaccae. U.S. Pat. No. 4,724,144 discloses an immunotherapeutic agent comprising antigenic material derived from M. vaccae for treatment of mycobacterial diseases, especially tuberculosis and leprosy, and as an adjuvant to chemotherapy. International Patent Publication WO 91/01751 discloses the use of antigenic and/or immunoregulatory material from M. vaccae as an immunoprophylactic to delay and/or prevent the onset of AIDS. International Patent Publication WO 94/06466 discloses the use of antigenic and/or immunoregulatory material derived from M. vaccae for therapy of HIV infection, with or without AIDS and with or without associated tuberculosis.
Traditional vaccines contain the disease-causing organism (or a component thereof) in either attenuated or killed form. As an alternative approach to traditional vaccines, DNA vaccines have been developed for diseases as diverse as AIDS, influenza, cancer and malaria. Clinical trials of DNA vaccines are in progress for a number of these diseases. A typical DNA vaccine consists of DNA encoding an antigen cloned in a non-active plasmid carrier. Expression of the antigen encoded by the vaccine DNA is usually under control of a strong promoter, such as human xcex2-actin, Rous sarcoma virus (RSV) or CMV promoter (Ramsay A J, Ramshaw I A, and Ada G L. Immunology and Cell Biology 75:360-363, 1997). The first experimental evidence that DNA vaccines were able to induce the desired immune response was produced by Tang et al. (Tang D-C, Devit M, Johnston S A. Nature 356:152-154, 1992). In these experiments, mice inoculated with plasmids containing the gene encoding for human growth hormone developed specific primary antibody responses.
Immune responses to two DNA vaccines containing genes from M. tuberculosis have been evaluated in animal models. The first vaccine contained the gene coding for the GroEL stress protein (65 kDa protein) (Tascon R E, Colston M J, Ragno S, Stavropoulos E, Gregory D, Lowrie D B. Nature Med. 2:888-892, 1996). Mice injected with this DNA vaccine were protected at a level equivalent to mice receiving the traditional BCG vaccine. The second DNA vaccine against M. tuberculosis contained DNA encoding an antigen from the antigen 85 complex and similar results to the study by Tang et al. were obtained (Huygen K, Content J, Denis O, Montgomery D L, Yawman A M, Deck R R, DeWitt C M, Orm I A, Baldwin S, D""Souza C, Drowart A, Lozes E, VandenBussche P, Van Vooren J -P, Liu M A and Ulmer J B. Nature Med. 2:893-898, 1996). U.S. Pat. No. 5,736,524 discloses vaccination of domestic mammals or livestock against infection by M. tuberculosis or M. bovis by administering a polynucleotide tuberculosis vaccine comprising the M. tuberculosis antigen 85 gene operably linked to transcription regulatory elements.
The first human DNA vaccine trial was reported recently (Wang R, Doolan D L, Le T P, Hedstrom R C, Coonan K M, Charoenvit Y, Jones T R, Hobart P, Margalith M, Ng J, Weiss W R, Sedegah M, de Taisne C, Norman J A, Hoffman S L. Science 282:476-80, 1998). In this trial, an antigen from Plasmodium falciparum, the causative agent of malaria, was injected into healthy volunteers. The desired immune response was elicited, as demonstrated by the presence of cytotoxic T (CD8+) lymphocytes (CTL), suggesting that the immune system would be able to clear parasites from infected patients. Safety and immunogenicity of a human DNA vaccine against HIV-1 infection was determined in a trial performed by McGregor et al. (MacGregor R R, Boyer J D, Ugen K E, Lacy K E, Gluckman S J, Bagarazzi M L, Chattergoon M A, Baine Y, Higgins T J, Ciccarelli R B, Coney L R, Ginsberg R S, Weiner D B. J. Infect. Dis. 178:92-100, 1998). Experimental data from other DNA vaccine experiments has also suggested that antibodies, MHC class 1-restricted CD8+ CTL and class II-restricted CD4+ helper T cells are produced following injection with DNA vaccines (Ramsay, A J, Ramshaw, I A and Ada, G L. Immunology and Cell Biology 75:360-363, 1997).
DNA vaccines have distinct advantages over more traditional vaccines containing killed or attenuated organisms. DNA vaccination induces immune responses that are long-lived and therefore only a single inoculation may be required. DNA encoding a number of antigens may be incorporated into a single plasmid thereby providing protection against a number of diseases. The technology for DNA vaccine production is relatively simple and the same technology can be used to produce all vaccines, with a resulting cheaper production cost. Delivery of efficacious traditional vaccines to the patient are dependent on maintaining an unbroken xe2x80x9ccold chainxe2x80x9d from manufacturer to clinic. DNA vaccines produced in solution or in dried form are not sensitive to storage conditions.
One limitation of DNA vaccines is that the immune response is induced against protein components of the pathogen, only. Some traditional vaccines are aimed at inducing an immune response against the polysaccharide outer membrane of pathogens, for example the pneumococcal vaccine against bacterial pneumonia. These molecules are not yet targeted by DNA vaccines.
Recently, alternative ways of constructing and applying DNA vaccines have been developed. In one of the techniques, called Somatic Transgene Immunisation (STI), the plasmid DNA carrying an immunoglobulin heavy chain gene under the control of tissue-specific regulatory elements was inoculated directly into the spleen of mice, with subsequent expression of the antigen on the surface of B-cells (Xiong S, Gerloni M, Zanetti M. Proc. Natl. Acad. Sci. USA 94:6352-6357, 1997). These B cells produced antibodies against the expressed antigen, leading to an immune response. Subsequent studies showed that STI induced persistent immunologic memory for up to 2 years (Gerloni M, Xiong S, Zanetti M. Vaccine (2-3):293-297, 1998).
Expression Library Immunization (ELI) is another technique employing DNA vaccines (Barry M A, Lai W C and Johnston, S A. Nature 377:632-635, 1995). In this technique, fragments of the complete genome of a pathogen are cloned into a vector and used as vaccine. Selection of protective antigen(s), particularly those inducing CTL, is done by screening and re-screening pools of clones until single clones can be identified. The polynucleotide or polypeptide identified may then be incorporated into a proven delivery system.
Progress on the development of an epitope-based vaccine for the treatment and prevention of HIV infection by scientists at Epimmune Inc. (San Diego, Calif.), has been published recently (Ishioka G Y, et al. Journal of Immunology 162:3915-3925, 1999).
There remains a need in the art for effective compounds and methods for preventing and treating infectious disorders, such as tuberculosis and other mycobacterial infections in humans and in domestic mammals or livestock, and for the treatment of certain immune system-related disorders.
Briefly stated, the present invention provides compounds and methods for the prevention and treatment of infectious diseases, such as mycobacterial infections, and for the treatment of immune disorders and cancers.
In a first aspect, isolated polynucleotides are provided that are derived front the M. vaccae genome. These polynucleotides encode polypeptide epitopes selected on the basis of their immunogenic properties as illustrated by results from a number of immunological assays. In specific embodiments, the inventive polynucleotides comprise a sequence selected from the group consisting of: (a) sequences provided in SEQ ID NO: 8-21; (b) sequences having at least 50%, 75% or 90% identical residues to a sequence of SEQ ID NO: 8-21 as determined using the computer algorithm BLASTN; and (c) compliments of the sequences of (a) and (b).
In a second aspect, the invention provides isolated polypeptides comprising an immunogenic epitope of a M. vaccae antigen. In specific embodiments, the inventive polypeptides comprise a sequence selected from the group consisting of: (a) sequences provided in SEQ ID NO: 61-77; and (b) sequences having at least 50%, 75% or 90% identical residues to a sequence of SEQ ID NO: 61-77 as determined using the computer algorithm FASTX.
DNA constructs comprising at least one of the inventive polynucleotides, and host cells transformed or transfected with such DNA constructs are also provided.
In another aspect, the present invention provides fusion proteins comprising at least one polypeptide of the present invention.
Within other aspects, the present invention provides pharmaceutical compositions that comprise at least one of the inventive polypeptides, polynucleotides, fusion proteins or DNA constructs, and a physiologically acceptable carrier The invention also provides vaccines comprising at least one of the above polypeptides, polynucleotides, fusion proteins or DNA constructs and a non-specific immune response amplifier.
In yet another aspect, methods are provided for enhancing an immune response in a patient, comprising administering to a patient an effective amount of one or more of the above pharmaceutical compositions and/or vaccines. In one embodiment, the immune response is a Th1 response.
In further aspects of this invention, methods are provided for the treatment of a disorder in a patient, comprising administering to the patient a pharmaceutical composition or vaccine of the present invention. In certain embodiments, the disorder is selected from the group consisting of immune disorders, infectious diseases and cancer.
These and other aspects of the present invention will become apparent upon reference to the following detailed description. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated individually.